[Bioperl-l] t/SimpleAlign: not ok 18
Jason Stajich
jason@cgt.mc.duke.edu
Thu, 12 Sep 2002 07:48:49 -0400 (EDT)
I cannot replicate on either the released tarball or current 1-0-0 branch
on IRIX with perl 5.6.1. Very strange. Can it be a 5.8.0 bug? That
seems odd but possible.
mendel 236% perl -V
Summary of my perl5 (revision 5.0 version 6 subversion 1) configuration:
Platform:
osname=irix, osvers=6.5, archname=IP27-irix
uname='irix64 mendel 6.5 10120104 ip27 '
config_args=''
hint=recommended, useposix=true, d_sigaction=define
usethreads=undef use5005threads=undef useithreads=undef
usemultiplicity=undef
useperlio=undef d_sfio=undef uselargefiles=define usesocks=undef
use64bitint=undef use64bitall=undef uselongdouble=undef
Compiler:
cc='cc -n32', ccflags ='-D_BSD_TYPES -D_BSD_TIME -woff
1009,1110,1174,1184,1552 -OPT:Olimit=0:space=ON -I/usr/local/include
-DLANGUAGE_C',
optimize='-O3',
cppflags='-D_BSD_TYPES -D_BSD_TIME -OPT:Olimit=0:space=ON
-I/usr/local/include -DLANGUAGE_C'
ccversion='', gccversion='', gccosandvers=''
intsize=4, longsize=4, ptrsize=4, doublesize=8, byteorder=4321
d_longlong=define, longlongsize=8, d_longdbl=define, longdblsize=16
ivtype='long', ivsize=4, nvtype='double', nvsize=8, Off_t='off_t',
lseeksize=8
alignbytes=8, usemymalloc=n, prototype=define
Linker and Libraries:
ld='cc -n32', ldflags ='-L/usr/lib32 -L/usr/freeware/lib32
-L/usr/local/lib32 -L/usr/local/lib -Wl,-woff,84'
libpth=/usr/local/lib /usr/lib32 /lib32 /lib /usr/lib
/usr/freeware/lib32
libs=-lgdbm -ldb -lm -lc
perllibs=-lm -lc
libc=/usr/lib32/libc.so, so=so, useshrplib=false, libperl=libperl.a
Dynamic Linking:
dlsrc=dl_dlopen.xs, dlext=so, d_dlsymun=undef, ccdlflags=' '
cccdlflags=' ', lddlflags='-n32 -shared -L/usr/lib32
-L/usr/freeware/lib32 -L/usr/local/lib32 -L/usr/local/lib'
Characteristics of this binary (from libperl):
Compile-time options: USE_LARGE_FILES
Built under irix
Compiled at Dec 13 2001 12:24:42
%ENV:
PERL5LIB="/v0/people/staji002/lib/lib/perl5"
@INC:
/v0/people/staji002/lib/lib/perl5/5.6.1
/v0/people/staji002/lib/lib/perl5
/usr/local/lib/perl5/5.6.1/IP27-irix
/usr/local/lib/perl5/5.6.1
/usr/local/lib/perl5/site_perl/5.6.1/IP27-irix
/usr/local/lib/perl5/site_perl/5.6.1
/usr/local/lib/perl5/site_perl
.
-jason
On Wed, 11 Sep 2002, Allen Smith wrote:
> t/SimpleAlign.............1..53
> ok 1
> ok 2
> ok 3
> ok 4
> ok 5
> ok 6
> ok 7
> ok 8
> ok 9
> ok 10
> ok 11
> ok 12
> ok 13
> ok 14
> ok 15
> ok 16
> ok 17
> not ok 18
> # Test 18 got: 'REELVYLAKLAEQAERYEEMVEFMKKVAESGASAEELSVEERNLLSVAYKNVIGARRASW' (t/SimpleAlign.t at line 53)
> # Expected: 'REDLVYLAKLAEQAERYEEMVEFMKKVAESGAPAEELSVEERNLLSVAYKNVIGARRASW'
> ok 19
> ok 20
> ok 21
> ok 22
> ok 23
> ok 24
> ok 25
> ok 26
> ok 27
> ok 28
> ok 29
> ok 30
> ok 31
> ok 32
> ok 33
> ok 34
> ok 35
> ok 36
> ok 37
> ok 38
> ok 39
> ok 40
> ok 41
> ok 42
> ok 43
> ok 44
> ok 45
> ok 46
> ok 47
> ok 48
> ok 49
> ok 50
> ok 51
> ok 52
> ok 53
> FAILED test 18
> Failed 1/53 tests, 98.11% okay
>
> bioperl-1.0.2.
>
> perl -V:
>
> Summary of my perl5 (revision 5.0 version 8 subversion 0) configuration:
> Platform:
> osname=irix, osvers=6.5, archname=IP30-R12000-irix-thread-multi-64int-ld
> uname='irix64 cesario 6.5 04101931 ip30 '
> config_args='-DDEBUGGING -Dusemorebits -Dcc=cc -n32 -mips4 -r12000 -TARG:platform=ip30:processor=r12000 -Wl,-woff,84 -woff 1009,1110,1047'
> hint=recommended, useposix=true, d_sigaction=define
> usethreads=define use5005threads=undef useithreads=define usemultiplicity=define
> useperlio=define d_sfio=undef uselargefiles=define usesocks=undef
> use64bitint=define use64bitall=undef uselongdouble=define
> usemymalloc=n, bincompat5005=undef
> Compiler:
> cc='cc -n32 -mips4 -r12000 -TARG:platform=ip30:processor=r12000 -Wl,-woff,84 -woff 1009,1110,1047', ccflags ='-DDEBUGGING -D_SGI_SOURCE -D_SGI_REENTRANT_FUNCTIONS -D_SGIAPI -D_POSIX1C -I/server/people/staff/easmith/include -DPTHREAD_H_FIRST -D_BSD_TYPES -D_BSD_TIME -woff 1184,1552 -I/usr/local/include -DLANGUAGE_C -DHAS_LDBL_SPRINTF_BUG -DHAS_LDBL_SPRINTF_BUG_LESS1',
> optimize='-O3 -OPT:fast_exp=ON:Olimit=0 -TENV:X=1 -LNO:opt=1:ou_further=3:gather_scatter=2 -OPT:fold_unsafe_relops=OFF:div_split=OFF:IEEE_arithmetic=1:roundoff=0 -OPT:got_call_conversion=OFF:space=OFF',
> cppflags='-DDEBUGGING -D_SGI_SOURCE -D_SGI_REENTRANT_FUNCTIONS -D_SGIAPI -D_POSIX1C -I/server/people/staff/easmith/include -DPTHREAD_H_FIRST -D_BSD_TYPES -D_BSD_TIME -I/usr/local/include -DLANGUAGE_C -DHAS_LDBL_SPRINTF_BUG -DHAS_LDBL_SPRINTF_BUG_LESS1'
> ccversion='MIPSpro Compilers: Version 7.3.1.3m', gccversion='', gccosandvers=''
> intsize=4, longsize=4, ptrsize=4, doublesize=8, byteorder=87654321
> d_longlong=define, longlongsize=8, d_longdbl=define, longdblsize=16
> ivtype='long long', ivsize=8, nvtype='long double', nvsize=16, Off_t='off_t', lseeksize=8
> alignbytes=16, prototype=define
> Linker and Libraries:
> ld='ld -mips4 -n32 -woff 84', ldflags ='-L/server/people/staff/easmith/lib32 -L/usr/lib32/mips4 -L/usr/lib32 -L/lib32 -rpath /server/people/staff/easmith/lib32:/usr/lib32/mips4:/usr/lib32:/lib32 -Wl,-woff,84'
> libpth=/server/people/staff/easmith/lib32 /usr/lib32/mips4 /usr/lib32 /lib32
> libs=-lgdbm -ldb -lm -lpthread
> perllibs=-lm -lpthread
> libc=/usr/lib32/libc.so, so=so, useshrplib=false, libperl=libperl.a
> gnulibc_version=''
> Dynamic Linking:
> dlsrc=dl_dlopen.xs, dlext=so, d_dlsymun=undef, ccdlflags=' '
> cccdlflags=' ', lddlflags='-shared -check_registry /usr/lib32/so_locations -L/server/people/staff/easmith/lib32 -L/usr/lib32/mips4 -L/usr/lib32 -L/lib32'
>
>
> Characteristics of this binary (from libperl):
> Compile-time options: DEBUGGING MULTIPLICITY USE_ITHREADS USE_64_BIT_INT USE_LONG_DOUBLE USE_LARGE_FILES PERL_IMPLICIT_CONTEXT
> Locally applied patches:
> DEVEL17807
> DEVEL17848
> DEVEL17874
> DEVEL17875
> DEVEL17881
> Built under irix
> Compiled at Sep 10 2002 20:11:45
> @INC:
> /usr/share/lib/perl5/5.8.0/IP30-R12000-irix
> /usr/share/lib/perl5/5.8.0
> /usr/share/lib/perl5/site_perl/5.8.0/IP30-R12000-irix
> /usr/share/lib/perl5/site_perl/5.8.0
> /usr/share/lib/perl5/site_perl/5.6.0
> /usr/share/lib/perl5/site_perl/5.005
> /usr/share/lib/perl5/site_perl
> .
>
>
> -Allen
>
>
--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu